Contacts of the helix formed by residues 161 - 167 (chain I) in PDB entry 7C97
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 161 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106I ILE* 3.6 19.1 - - + -
110I TRP* 3.4 34.5 - - + -
139I ILE* 5.5 1.3 - - + -
143I PHE* 5.2 7.9 - - + -
149I PHE* 3.4 35.9 - - + -
157I VAL 4.1 9.4 - - - +
158I ASP* 2.9 9.2 + - - +
160I TYR* 1.3 80.2 - - - +
162I ALA* 1.3 54.3 + - - +
163I PRO 3.4 0.2 - - - -
164I LEU* 2.7 11.4 + - + -
165I LEU* 2.5 55.2 + - + +
186I TYR* 4.4 16.8 - - - +
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Residues in contact with ALA 162 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I ILE* 5.1 2.9 - - + -
154I PHE* 6.4 1.6 - - + -
158I ASP 3.3 8.7 + - - +
159I CYS* 5.1 2.2 - - - -
161I LEU* 1.3 77.6 - - - +
163I PRO* 1.3 61.8 - - + +
165I LEU* 2.8 13.0 + - - +
166I TRP* 2.5 38.2 + - - +
190I VAL* 4.1 26.5 - - + -
191I PHE* 4.0 3.9 - - + -
196I PHE* 4.4 17.7 - - + -
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Residues in contact with PRO 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I ILE* 3.2 33.6 - - + +
23I HIS* 3.9 22.9 - - + +
24I GLN* 4.0 7.4 - - + -
27I ILE* 3.3 29.2 - - + -
159I CYS 3.0 26.9 - - - +
161I LEU 3.9 0.7 - - - -
162I ALA* 1.3 88.2 - - + +
164I LEU* 1.3 57.5 + - - +
165I LEU 3.2 0.2 - - - -
166I TRP* 3.5 15.3 + - + +
167I ARG* 3.3 18.9 + - - +
196I PHE* 5.4 0.2 - - + -
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Residues in contact with LEU 164 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ILE* 3.3 25.8 - - + -
24I GLN* 4.4 2.0 - - - +
106I ILE* 3.7 19.1 - - + -
110I TRP* 4.7 10.5 - - + +
111I TYR* 3.3 39.9 - - + -
114I MET* 4.0 32.1 - - + +
136I LEU* 6.0 0.9 - - - +
160I TYR 3.2 19.0 + - - +
161I LEU* 2.7 16.5 + - + +
163I PRO* 1.3 73.8 - - - +
165I LEU* 1.3 63.7 + - - +
167I ARG* 4.4 13.4 + - - +
168I LEU* 5.0 1.2 + - - -
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Residues in contact with LEU 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I TRP* 6.3 0.9 - - + -
136I LEU* 4.9 19.5 - - + -
143I PHE* 6.3 0.4 - - + -
161I LEU* 2.5 43.5 + - + +
162I ALA* 2.8 6.5 + - - +
164I LEU* 1.3 78.4 - - - +
166I TRP* 1.3 58.8 + - - +
167I ARG 3.4 2.0 - - - -
168I LEU* 3.9 27.5 - - + +
175I PHE* 5.2 8.7 - - + -
183I LEU* 5.1 8.5 - - + -
186I TYR* 4.4 21.8 - - + +
187I MET* 4.8 11.2 - - + +
190I VAL* 6.5 0.4 - - + -
191I PHE* 3.0 34.0 - - + -
208I ARG* 4.8 1.4 + - - -
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Residues in contact with TRP 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23I HIS* 4.2 8.3 - + - -
162I ALA 2.5 17.2 + - - +
163I PRO* 3.5 10.0 + - + +
165I LEU* 1.3 72.9 - - - +
167I ARG* 1.3 60.4 + - + +
168I LEU 3.3 5.2 - - - -
169I PRO* 4.8 0.2 - - - +
170I GLN* 5.1 2.1 - - - +
191I PHE* 3.4 36.3 - + + -
196I PHE* 4.1 10.3 - + + -
200I LEU* 3.3 43.9 - - + +
204I GLU* 2.9 32.3 + - + +
205I ARG* 3.7 22.7 - - + -
207I MET* 5.6 2.8 - - - +
208I ARG* 3.2 68.2 + - + -
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Residues in contact with ARG 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I THR* 2.2 37.6 + - - +
19I ASP 3.6 0.4 - - - -
20I ILE* 3.2 51.3 - - - +
23I HIS* 4.3 14.1 + - - +
114I MET* 4.0 29.8 - - + +
163I PRO 3.3 15.3 + - - +
164I LEU* 5.0 7.2 - - - -
165I LEU* 3.4 1.5 - - - +
166I TRP* 1.3 81.7 - - + +
168I LEU* 1.3 64.4 + - - +
169I PRO 3.7 1.1 - - - -
170I GLN* 3.7 34.1 + - + +
171I LEU* 3.9 7.0 + - - +
173I ILE* 5.2 0.7 - - - +
204I GLU* 2.8 26.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il